Membraneless Organelles and Wisdom of the Crowds: Novel Mechanisms Underlying Gene Regulation in Bacteria

The poles of rod-shaped bacteria emerge as hubs for sensing and regulation. The poles have been shown by our lab to be enriched for regulatory small RNAs (sRNAs). Upon osmotic stress, the level of numerous sRNAs, most of them not known to be involved in the applied stress, dramatically increases at the poles, and they are accompanied by their chaperon Hfq (Mol. Cell, 2019).

Bioinformatic analysis of RNA-seq datasets of different bacterial species exposed to antibiotics or infection-relevant conditions revealed changes in numerous sRNAs, suggesting the existence of a polygenic plan for sRNA-mediated regulation. To test this hypothesis, we deleted groups of sRNAs and tested for fitness defects under stress. A significant defect was observed only when a handful of pole-enriched sRNAs were co-deleted. Cooperative activity of large sets of sRNAs explains the subtle effects of deleting single sRNAs considered important for bacterial physiology and virulence (iScience, 2021).

My recent results show that the sRNA chaperon Hfq undergoes phase separation in an RNA-dependent manner. Under normal conditions, Hfq forms foci scattered in a helical pattern along the cell length, but upon certain stresses it forms condensates at the poles. Notably, phase separation of Hfq is important for its roles as sRNAs stabilizer and sRNA-mRNA matchmaker. Relocation of Hfq to the poles and sRNA accumulation under stress depend on the novel pole localizer TmaR.

Our results provide evidence for spatiotemporal and polygenic plans underlying sRNA-mediated regulation in response to environmental cues, with the cell poles providing an arena for their implementation.